Table 1.
Epigenetic editing technologies for gene transcriptional activation
| Gene regulation: ACTIVATION | Effector domain (ED) | Molecular function | Targeted genomic region | Epigenetic technology (direct ED fusion) | Epigenetic technology (ED recruitment) |
|---|---|---|---|---|---|
| Recruiters of endogenous transcriptional activators | VP16 Virion protein 16, from herpes simplex (minimal unit) | DNA demethylation Increased H3K27ac and H3K4me | Gene promoters | ZFP (24,25) | ZFP (GI-LOV) (124) |
| VP48 (3 × VP16) | DNA demethylation Increased H3K27ac and H3K4me | Gene promoters | SpdCas9 (38) | ||
| VP64 (tetrameric repeat of VP16) | DNA demethylation Increased H3K27ac and H3K4me | Gene promoters and enhancers | ZFP (26,27,32,40,83) TALE (9,29,33,37) SpdCas9 (30,34–37,41,66,134,254,259) SadCas9 (251) | TALE-SunTag (43) TALE-LITE (120) SpdCas9 split (Fkbp/Frb) (122) SpdCas9 (MS2-MCP) (117) SpdCas9 (MS2-MCP) (DHFR-DD and AID systems) (128) SpdCas9 (LACE) (126) SpdCas9-SunTag (42,44,45) LbdCas12a-SunTag (23) | |
| VP160 (10 tandem copies of VP16 motif) | DNA demethylation Increased H3K27ac and H3K4me | Gene promoters | SpdCas9 (38) | ||
| VP192 (12 tandem copies of VP16 motif) | DNA demethylation Increased H3K27ac and H3K4me | Gene promoters | SpdCas9 (DHFR-DD system) (127) | ||
| p65 (major subunit of NF-kB transcription factor) | Increased H3K9ac and H3K14ac | Gene promoters | ZFP (25,28) TALE (29) SpdCas9 (30) | ZFP (Fkbp/Frb) (121) LbdCas12a (DmrA/DmrC) (22) | |
| p65-HSF1 (p65 and Heat shock factor 1) | Increased H3K4me3 and H3K27ac | Gene promoters | SpdCas9 (MS2-MCP) (250) | ||
| VP64, p65-HSF1 Synergistic activation mediator (SAM) (Enhanced gene activation) | Not evaluated | Gene promoters | SpdCas9 (MS2-MCP) (46–48) | ||
| VPR VP64, p65, Rta (Enhanced gene activation) | Not evaluated | Gene promoters and enhancers | SpdCas9 (49,51–54,133,235,258) SadCas9 (253) Sp and Sa dCas9 (19) enAsdCas12a (232) PaeCascade (234) | Sp and Nme dCas9 (Fkbp/Frb) and (GAI/GID1) (119) Sp and Sa dCas9 (GAI/GID1) and (ABI/PYL1) (18) LbdCas12a (DmrA/DmrC) (22) | |
| VPH VP64, p65, HSF1 (Enhanced gene activation) | Not evaluated | Gene promoters | Sp and Sa dCas9-SunTag (4-OHT) (123) | ||
| Enzymes: DNA demethylation | TET1 Ten-Eleven Translocation 1 catalytic domain (CD) | Methylcytosine dioxygenase 1 Decreased cytosine methylation (5mC) (eraser) | Gene promoters and enhancers | ZFP and TALE (58) SpdCas9 (60–62,66) SadCas9 (19) | TALE (CRY2-CIB1) (125) SpdCas9 (MS2-MCP) (63) SpdCas9-SunTag (64) |
| lncRNA promoters | TALE (59) | ||||
| Major satellite repeats | SpdCas9 (GBP-GFP) (65) | ||||
| TET2 Ten-Eleven Translocation 2 (CD) | Methylcytosine dioxygenase 2 Decreased 5mC (eraser) | Gene promoters | ZFP (55,56) | ||
| TDG Thymine DNA glycosylase | Recognizes and binds 5fC and 5caC and mediates base-excision repair (BER) (eraser) | Gene promoters | ZFP (57) | ||
| TET1-CD and VP64 (Enhanced gene activation) | DNA Demethylation Increased H3K27ac and H3K4me | Gene promoters | SpdCas9-SunTag (247) | ||
| TET1-CD and GADD45A or NEIL2 (Enhanced gene activation) | DNA demethylation coupled with BER machinery (eraser) | Gene promoters | SpdCas9 (Casilio system) (67) | ||
| Multiple distinct EDs for epigenetic memory | TET1-CD and VPR | Long-term gene activation DNA demethylation coupled with VPR activator | Gene promoters | Sa and Sp dCas9 (19) | |
| Enzymes: Histone lysine acetylation | p300 (catalytic domain) | Histone lysine acetyltransferase (KAT) Increased H3K27ac (writer) | Gene promoters and enhancers | ZFP, TALE, and Sp and Nme dCas9 (69) SpdCas9 (70,135) LbdCas12a (23) EcoCascade (233) | |
| Putative regulatory elements | SpdCas9 (71) SpdCas9 (AID system) (129) | ||||
| CBP (CREB-binding protein domain) | Histone lysine acetyltransferase (KAT) Increased H3K27ac (writer) | Gene promoters and enhancers | SpdCas9 (Casilio system) (68) | ||
| GCN5 (General Control Of Amino Acid Synthesis Protein 5-Like 2) | Histone lysine acetyltransferase (KAT) Increased H3K9ac and H3K14ac (writer) | Gene promoters | SpdCas9 (72) | ||
| Chromatin readers | BRD4 Bromodomain containing 4 | Recognizes and binds acetylated histones, i.e., H4K5ac and H4K8ac (reader) | Gene promoters | SpdCas9 (73) | |
| Chromatin remodelers | Ldb1 LIM domain binding protein 1 (Self-association domain) | Recruitment of enhancer-associated endogenous Ldb1 Forced looping between promoter and enhancer | Gene promoters and enhancers | ZFP (74) TALE (75) | |
| Enzymes: Histone lysine methylation | PRDM9 (PR/SET Domain 9) | Histone lysine methyltransferase (KMT) Increased H3K4me3 (writer) | Gene promoters | ZFP and SpdCas9 (76) | |
| DOT1L (DOT1 Like) | Histone lysine methyltransferase (KMT) Increased H3K79me2 and 3 (writer) | Gene promoters | ZFP and SpdCas9 (76) | ||
| MLL3SET (Myeloid/Lymphoid Or Mixed-Lineage Leukemia Protein 3 SET domain) | Histone lysine methyltransferase (KMT) Increased H3K4me1 (writer) Recruitment of p300 Increased H3K27ac | Super enhancers | SpdCas9 (77) | ||
| SMYD3 (SET and MYND Domain Containing 3) | Histone lysine methyltransferase (KMT) Increased H3K4me3 (writer) | Gene promoters | SpdCas9 (78) | ||
| Multiple distinct EDs for epigenetic memory | PRDM9 and DOT1L | Long-term gene activation Increased H3K4me3 and H3K79me2 and 3 | Gene promoters | SpdCas9 (76) |
Abbreviations: H3: histone 3; K: lysine; ac: acetylation; me: methylation; me2: di-methylated state; me3: tri-methylated state; ZFP: zinc-finger proteins; GI: GIGANTEA; LOV: light oxygen voltage domain of FKF1; TALE: transcription activator-like effector; Sp: Streptococcus pyogenes; Sa: Staphylococcus aureus; dCas9: catalytically deactivated Cas9 protein; SunTag: SUperNova Tagging; LITE: Light-Inducible Transcriptional Effector; FKBP: FK506-binding protein; FRB: FKBP–rapamycin binding; MS2: RNA aptamer; MCP: MS2-coat protein; LACE: Light-Activated CRISPR-dCas9 Effector; Lb: Lachnospiraceae bacterium; dCas12a: catalytically deactivated Cas12a protein; DHFR-DD system: dihydrofolate reductase (DHFR)-derived destabilization domain; Rta: replication and transcription activator; en: enhanced; As: Acidaminococcus sp.; Pae: Pseudomonas aeruginosa; Cascade: CRISPR-associated complex for antiviral defense; DmrA: FKBP domain; DmrC: FRB domain; Nme: Neisseria meningitidis; GAI: gibberellin (GA) insensitive protein; GID1: gibberellin-insensitive dwarf1 protein; ABI: abscisic acid (ABA)-insensitive 1 protein; PYL1: abscisic acid receptor; 4-OHT: 4-Hydroxytamoxifen; 5mC: 5-methylcytosine; CRY2: cryptochrome 2; CIB1: cryptochrome-2-interacting binding protein-1; lncRNA: long non-coding RNAs; GFP: green fluorescent protein; GBP: GFP-binding protein; 5fC: 5-formylcytosine; 5caC: 5-carboxylcytosine; GADD45A: Growth Arrest and DNA-Damage-inducible Alpha; NEIL2: Nei-Like DNA Glycosylase 2; Eco: Escherichia coli; AID: Auxin-Inducible Degron; H4: histone 4.